Targeted genome sequencing by the next generation sequencing (NGS) technology has become a powerful platform for biomedical and agricultural genome analyses, such as human identity and ancestry identification, disease diagnostics, plant germplasm molecular characterization, and molecular breeding. While the capacity of NGS platforms advances rapidly, the preparation of NGS-ready DNA libraries has become a limiting factor. Multiplex PCR is an ideal platform for high throughput production of DNA libraries. However, as the number of primer pairs increases drastically from a few pairs to several hundred or even several thousand pairs in a single reaction, primer dimer formation during multiplex PCR and the interference of the resultant primer dimers in the subsequent library preparation steps become an obstacle to successful NGS applications. Thus, there is a need for methods, compositions, and kits for preparing DNA sequencing libraries in a streamlined, high throughput, and low cost manner for both biomedical and agricultural applications.